From 6f44a7e4dbc580af826dd0264d4f8e56bf28eff2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 21 Oct 2026 02:54:22 +0000
Subject: [PATCH 1/2] Initial plan


From 6303399634b815de2b4d6e65c520eb854ce695ac Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 21 Oct 2026 03:23:25 +0000
Subject: [PATCH 2/2] Apply remaining changes

Co-authored-by: chemplexity <5705840+chemplexity@users.noreply.github.com>
---
 src/layout/engine/cleanup/stage-runner.js  | 16 +++++++++++++++-
 src/layout/engine/cleanup/symmetry-tidy.js | 10 ++++++++++
 src/layout/engine/pipeline.js              |  6 +++++-
 3 files changed, 30 insertions(+), 2 deletions(-)

diff --git a/src/layout/engine/cleanup/stage-runner.js b/src/layout/engine/cleanup/stage-runner.js
index e74753ac..85baa0ef 100644
--- a/src/layout/engine/cleanup/stage-runner.js
+++ b/src/layout/engine/cleanup/stage-runner.js
@@ -135,6 +135,20 @@ function resolveParentStageResult(stageResults, baselineStage, parentStage, best
   return null;
 }
 
+function movesFixedAtoms(layoutGraph, parentCoords, candidateCoords) {
+  if (!layoutGraph || layoutGraph.options?.preserveFixed === false || !(layoutGraph.fixedCoords?.size > 0)) {
+    return false;
+  }
+  for (const atomId of layoutGraph.fixedCoords.keys()) {
+    const before = parentCoords.get(atomId);
+    const after = candidateCoords.get(atomId);
+    if (before && after && (before.x !== after.x || before.y !== after.y)) {
+      return true;
+    }
+  }
+  return false;
+}
+
 /**
  * Executes a cleanup-stage DAG while tracking the current incumbent and stage sidecars.
  * @param {object[]} stages - Ordered stage descriptors.
@@ -209,7 +223,7 @@ export function runStageGraph(stages, baselineStage, context, seedState = null)
     }
 
     const prevBestStage = bestStage;
-    const accepted = !stage.comparatorFn || stage.comparatorFn(stageResult, bestStage, context, stageResults);
+    const accepted = !movesFixedAtoms(context.layoutGraph, parentStageResult.coords, stageResult.coords) && (!stage.comparatorFn || stage.comparatorFn(stageResult, bestStage, context, stageResults));
     stageExecution.accepted = accepted;
     if (accepted) {
       bestStage = stageResult;
diff --git a/src/layout/engine/cleanup/symmetry-tidy.js b/src/layout/engine/cleanup/symmetry-tidy.js
index d3895b25..8a702a51 100644
--- a/src/layout/engine/cleanup/symmetry-tidy.js
+++ b/src/layout/engine/cleanup/symmetry-tidy.js
@@ -7,6 +7,10 @@ import { angleOf, angularDifference, centroidForAtomIds, rotate, sub } from '../
 const IDEMPOTENT_AXIS_EPSILON = 1e-12;
 const LOCAL_AXIS_SNAP_ANGLE_EPSILON = Math.PI / 720;
 
+function isFixedAtom(layoutGraph, atomId) {
+  return layoutGraph?.options?.preserveFixed !== false && layoutGraph?.fixedCoords?.has(atomId) === true;
+}
+
 /**
  * Returns the qualifying fused ring-junction pairs that should be snapped to an axis.
  * @param {object} layoutGraph - Layout graph shell.
@@ -43,6 +47,9 @@ function collectJunctionTargets(layoutGraph) {
     if (!component) {
       continue;
     }
+    if (component.atomIds.some(atomId => isFixedAtom(layoutGraph, atomId))) {
+      continue;
+    }
     if (!targets.has(component.id)) {
       targets.set(component.id, {
         atomIds: [...component.atomIds],
@@ -330,6 +337,9 @@ export function tidySymmetry(inputCoords, options = {}) {
 
   for (const [atomId, position] of junctionSnap.coords) {
     const nextPosition = { ...position };
+    if (isFixedAtom(options.layoutGraph, atomId)) {
+      continue;
+    }
     if (Math.abs(nextPosition.x) <= epsilon) {
       const snappedPosition = { ...nextPosition, x: 0 };
       if (!wouldAxisSnapDistortLocalGeometry(options.layoutGraph, coords, atomId, snappedPosition)) {
diff --git a/src/layout/engine/pipeline.js b/src/layout/engine/pipeline.js
index 211b6836..fcf139d9 100644
--- a/src/layout/engine/pipeline.js
+++ b/src/layout/engine/pipeline.js
@@ -16600,6 +16600,7 @@ export function runPipeline(molecule, options = {}) {
       const postRoutingLargeDirtyResidualRetouch = timeFinalRetouch('postRoutingLargeDirtyResidualRetouch', () =>
         runLargeMoleculeResidualRetouch(layoutGraph, finalCoords, {
           bondLength: normalizedOptions.bondLength,
+          frozenAtomIds: placement.frozenAtomIds,
           residualOnly: true
         })
       );
@@ -16827,7 +16828,8 @@ export function runPipeline(molecule, options = {}) {
   if (placement.placedFamilies.includes('large-molecule') || familySummary.primaryFamily === 'large-molecule') {
     const largeMoleculeResidualRetouch = timeFinalRetouch('largeMoleculeResidualRetouch', () =>
       runLargeMoleculeResidualRetouch(layoutGraph, finalCoords, {
-        bondLength: normalizedOptions.bondLength
+        bondLength: normalizedOptions.bondLength,
+        frozenAtomIds: placement.frozenAtomIds
       })
     );
     if (largeMoleculeResidualRetouch.changed) {
@@ -18623,6 +18625,7 @@ export function runPipeline(molecule, options = {}) {
       const lateLargeMoleculeResidualRetouch = timeFinalRetouch('lateLargeMoleculeResidualRetouch', () =>
         runLargeMoleculeResidualRetouch(layoutGraph, finalCoords, {
           bondLength: normalizedOptions.bondLength,
+          frozenAtomIds: placement.frozenAtomIds,
           residualOnly: true
         })
       );
@@ -18711,6 +18714,7 @@ export function runPipeline(molecule, options = {}) {
       const finalLargeMoleculeResidualRetouch = timeFinalRetouch('finalLargeMoleculeResidualRetouch', () =>
         runLargeMoleculeResidualRetouch(layoutGraph, finalCoords, {
           bondLength: normalizedOptions.bondLength,
+          frozenAtomIds: placement.frozenAtomIds,
           residualOnly: true
         })
       );